Project name: 0209-00002_ChargedMuts

Status: done

Started: 2025-12-09 19:20:44
Chain sequence(s) H: QVQLVQSGAEVKKPGASVKVSCKASGYTFTSYAMHWVRQAPGQRLEWMGWINAGNGNTKYSQKFQGRVTITRDTSASTAYMELSSLRSEDTAVYYCARRGSGWYPDYWGQGTLVTVSS
L: NIQMTQSPSSLSASVGDRVTITCQASQDISNYLNWYQQKPGKAPKLLIYDASNLETGVPSRFSGSGSGTDFTFTISSLQPEDIATYYCQHYDNLPLTFGGGTKVDIK
input PDB
Selected Chain(s) H,L
Distance of aggregation 10 Å
FoldX usage Yes
pH calculations No
alphaCutter usage No
Dynamic mode No
Automated mutations Yes
Downloads Download all the data
Simulation log 
[INFO]       Logger:   Verbosity set to: 2 - [INFO]                                                (00:00:02)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:02)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with all chain(s) selected           (00:00:02)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:02)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:02)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:02:31)
[INFO]       AutoMut:  Residue number 28 from chain H and a score of 0.836 (tyrosine) selected for 
                       automated mutation                                                          (00:02:33)
[INFO]       AutoMut:  Residue number 123 from chain H and a score of 0.512 (leucine) selected for 
                       automated mutation                                                          (00:02:33)
[INFO]       AutoMut:  Residue number 29 from chain H and a score of 0.491 (threonine) selected    
                       for automated mutation                                                      (00:02:33)
[INFO]       AutoMut:  Residue number 101 from chain H and a score of 0.465 (valine) selected for  
                       automated mutation                                                          (00:02:33)
[INFO]       AutoMut:  Residue number 12 from chain H and a score of 0.347 (valine) selected for   
                       automated mutation                                                          (00:02:33)
[INFO]       AutoMut:  Residue number 15 from chain L and a score of 0.315 (valine) selected for   
                       automated mutation                                                          (00:02:33)
[INFO]       AutoMut:  Mutating residue number 28 from chain H (tyrosine) into glutamic acid       (00:02:33)
[INFO]       AutoMut:  Mutating residue number 123 from chain H (leucine) into glutamic acid       (00:02:33)
[INFO]       AutoMut:  Mutating residue number 28 from chain H (tyrosine) into aspartic acid       (00:02:33)
[INFO]       AutoMut:  Mutating residue number 28 from chain H (tyrosine) into arginine            (00:02:48)
[INFO]       AutoMut:  Mutating residue number 123 from chain H (leucine) into lysine              (00:02:50)
[INFO]       AutoMut:  Mutating residue number 28 from chain H (tyrosine) into lysine              (00:02:51)
[INFO]       AutoMut:  Mutating residue number 123 from chain H (leucine) into aspartic acid       (00:03:19)
[INFO]       AutoMut:  Mutating residue number 29 from chain H (threonine) into glutamic acid      (00:03:29)
[INFO]       AutoMut:  Mutating residue number 123 from chain H (leucine) into arginine            (00:03:31)
[INFO]       AutoMut:  Mutating residue number 29 from chain H (threonine) into aspartic acid      (00:03:47)
[INFO]       AutoMut:  Mutating residue number 29 from chain H (threonine) into lysine             (00:03:48)
[INFO]       AutoMut:  Mutating residue number 101 from chain H (valine) into glutamic acid        (00:03:59)
[INFO]       AutoMut:  Mutating residue number 29 from chain H (threonine) into arginine           (00:03:59)
[INFO]       AutoMut:  Mutating residue number 101 from chain H (valine) into aspartic acid        (00:04:12)
[INFO]       AutoMut:  Mutating residue number 101 from chain H (valine) into lysine               (00:04:15)
[INFO]       AutoMut:  Mutating residue number 12 from chain H (valine) into glutamic acid         (00:04:23)
[INFO]       AutoMut:  Mutating residue number 101 from chain H (valine) into arginine             (00:04:25)
[INFO]       AutoMut:  Mutating residue number 12 from chain H (valine) into lysine                (00:04:36)
[INFO]       AutoMut:  Mutating residue number 12 from chain H (valine) into aspartic acid         (00:04:49)
[INFO]       AutoMut:  Mutating residue number 15 from chain L (valine) into glutamic acid         (00:04:51)
[INFO]       AutoMut:  Mutating residue number 15 from chain L (valine) into aspartic acid         (00:04:59)
[INFO]       AutoMut:  Mutating residue number 12 from chain H (valine) into arginine              (00:05:01)
[INFO]       AutoMut:  Mutating residue number 15 from chain L (valine) into lysine                (00:05:04)
[INFO]       AutoMut:  Mutating residue number 15 from chain L (valine) into arginine              (00:05:13)
[INFO]       AutoMut:  Effect of mutation residue number 28 from chain H (tyrosine) into glutamic  
                       acid: Energy difference: 0.9518 kcal/mol, Difference in average score from  
                       the base case: -0.0398                                                      (00:05:40)
[INFO]       AutoMut:  Effect of mutation residue number 28 from chain H (tyrosine) into lysine:   
                       Energy difference: 0.7570 kcal/mol, Difference in average score from the    
                       base case: -0.0358                                                          (00:05:40)
[INFO]       AutoMut:  Effect of mutation residue number 28 from chain H (tyrosine) into aspartic  
                       acid: Energy difference: 0.7976 kcal/mol, Difference in average score from  
                       the base case: -0.0392                                                      (00:05:40)
[INFO]       AutoMut:  Effect of mutation residue number 28 from chain H (tyrosine) into arginine: 
                       Energy difference: 0.8248 kcal/mol, Difference in average score from the    
                       base case: -0.0434                                                          (00:05:40)
[INFO]       AutoMut:  Effect of mutation residue number 123 from chain H (leucine) into glutamic  
                       acid: Energy difference: 0.4540 kcal/mol, Difference in average score from  
                       the base case: -0.0342                                                      (00:05:40)
[INFO]       AutoMut:  Effect of mutation residue number 123 from chain H (leucine) into lysine:   
                       Energy difference: 0.0913 kcal/mol, Difference in average score from the    
                       base case: -0.0354                                                          (00:05:40)
[INFO]       AutoMut:  Effect of mutation residue number 123 from chain H (leucine) into aspartic  
                       acid: Energy difference: 1.3615 kcal/mol, Difference in average score from  
                       the base case: -0.0300                                                      (00:05:40)
[INFO]       AutoMut:  Effect of mutation residue number 123 from chain H (leucine) into arginine: 
                       Energy difference: 0.0147 kcal/mol, Difference in average score from the    
                       base case: -0.0415                                                          (00:05:40)
[INFO]       AutoMut:  Effect of mutation residue number 29 from chain H (threonine) into glutamic 
                       acid: Energy difference: -0.4676 kcal/mol, Difference in average score from 
                       the base case: -0.0233                                                      (00:05:40)
[INFO]       AutoMut:  Effect of mutation residue number 29 from chain H (threonine) into lysine:  
                       Energy difference: -0.2694 kcal/mol, Difference in average score from the   
                       base case: -0.0208                                                          (00:05:40)
[INFO]       AutoMut:  Effect of mutation residue number 29 from chain H (threonine) into aspartic 
                       acid: Energy difference: -0.7966 kcal/mol, Difference in average score from 
                       the base case: -0.0224                                                      (00:05:40)
[INFO]       AutoMut:  Effect of mutation residue number 29 from chain H (threonine) into          
                       arginine: Energy difference: -0.5003 kcal/mol, Difference in average score  
                       from the base case: -0.0224                                                 (00:05:40)
[INFO]       AutoMut:  Effect of mutation residue number 101 from chain H (valine) into glutamic   
                       acid: Energy difference: 0.8151 kcal/mol, Difference in average score from  
                       the base case: -0.0154                                                      (00:05:40)
[INFO]       AutoMut:  Effect of mutation residue number 101 from chain H (valine) into lysine:    
                       Energy difference: 0.0127 kcal/mol, Difference in average score from the    
                       base case: -0.0196                                                          (00:05:40)
[INFO]       AutoMut:  Effect of mutation residue number 101 from chain H (valine) into aspartic   
                       acid: Energy difference: 0.9654 kcal/mol, Difference in average score from  
                       the base case: -0.0177                                                      (00:05:40)
[INFO]       AutoMut:  Effect of mutation residue number 101 from chain H (valine) into arginine:  
                       Energy difference: 0.0545 kcal/mol, Difference in average score from the    
                       base case: -0.0231                                                          (00:05:40)
[INFO]       AutoMut:  Effect of mutation residue number 12 from chain H (valine) into glutamic    
                       acid: Energy difference: 0.3264 kcal/mol, Difference in average score from  
                       the base case: -0.0577                                                      (00:05:40)
[INFO]       AutoMut:  Effect of mutation residue number 12 from chain H (valine) into lysine:     
                       Energy difference: -0.2328 kcal/mol, Difference in average score from the   
                       base case: -0.0542                                                          (00:05:40)
[INFO]       AutoMut:  Effect of mutation residue number 12 from chain H (valine) into aspartic    
                       acid: Energy difference: 0.7622 kcal/mol, Difference in average score from  
                       the base case: -0.0568                                                      (00:05:40)
[INFO]       AutoMut:  Effect of mutation residue number 12 from chain H (valine) into arginine:   
                       Energy difference: -0.1100 kcal/mol, Difference in average score from the   
                       base case: -0.0564                                                          (00:05:40)
[INFO]       AutoMut:  Effect of mutation residue number 15 from chain L (valine) into glutamic    
                       acid: Energy difference: -0.0411 kcal/mol, Difference in average score from 
                       the base case: -0.0510                                                      (00:05:40)
[INFO]       AutoMut:  Effect of mutation residue number 15 from chain L (valine) into lysine:     
                       Energy difference: -1.7515 kcal/mol, Difference in average score from the   
                       base case: -0.0510                                                          (00:05:40)
[INFO]       AutoMut:  Effect of mutation residue number 15 from chain L (valine) into aspartic    
                       acid: Energy difference: 0.0137 kcal/mol, Difference in average score from  
                       the base case: -0.0507                                                      (00:05:40)
[INFO]       AutoMut:  Effect of mutation residue number 15 from chain L (valine) into arginine:   
                       Energy difference: -1.3712 kcal/mol, Difference in average score from the   
                       base case: -0.0532                                                          (00:05:40)
[INFO]       Main:     Simulation completed successfully.                                          (00:05:48)
Show buried residues
Minimal score value
-2.8105
Maximal score value
0.8357
Average score
-0.7218
Total score value
-162.4151
Download the table (csv)

The table below lists A4D score for protein residues. Residues with A4D score > 0.0000 are marked by yellow rows.

residue index residue name chain Aggrescan4D score mutation
1 Q H -0.9753
2 V H -0.0955
3 Q H -0.8158
4 L H 0.0000
5 V H 0.2793
6 Q H -0.3329
7 S H -0.8103
8 G H -0.5925
9 A H -0.4112
11 E H -1.1914
12 V H 0.3466
13 K H -1.1748
14 K H -2.1704
15 P H -2.0634
16 G H -1.5550
17 A H -1.2456
18 S H -1.2852
19 V H 0.0000
20 K H -2.0983
21 V H 0.0000
22 S H -0.7427
23 C H 0.0000
24 K H -1.1740
25 A H 0.0000
26 S H -0.4321
27 G H -0.2937
28 Y H 0.8357
29 T H 0.4907
30 F H 0.0000
35 T H -0.4754
36 S H -0.3487
37 Y H 0.0356
38 A H 0.0000
39 M H 0.0000
40 H H 0.0000
41 W H 0.0000
42 V H 0.0000
43 R H 0.0000
44 Q H -0.9322
45 A H -1.2472
46 P H -1.0143
47 G H -1.5777
48 Q H -2.5103
49 R H -2.7201
50 L H 0.0000
51 E H -1.0695
52 W H 0.0000
53 M H 0.0000
54 G H 0.0000
55 W H 0.0000
56 I H 0.0000
57 N H -2.1094
58 A H 0.0000
59 G H -1.7009
62 N H -2.4098
63 G H -2.1820
64 N H -2.6368
65 T H -1.9171
66 K H -2.2657
67 Y H -1.6940
68 S H 0.0000
69 Q H -2.7274
70 K H -2.6797
71 F H 0.0000
72 Q H -2.4842
74 G H -1.5974
75 R H -1.2788
76 V H 0.0000
77 T H -0.8939
78 I H 0.0000
79 T H -0.6769
80 R H -1.1799
81 D H -0.9051
82 T H -0.6308
83 S H -0.4214
84 A H -0.5506
85 S H -0.6446
86 T H -0.6887
87 A H 0.0000
88 Y H -0.7081
89 M H 0.0000
90 E H -1.2317
91 L H 0.0000
92 S H -1.0532
93 S H -1.2126
94 L H 0.0000
95 R H -2.8105
96 S H -2.2414
97 E H -2.4577
98 D H 0.0000
99 T H -0.6059
100 A H 0.0000
101 V H 0.4647
102 Y H 0.0000
103 Y H 0.0000
104 C H 0.0000
105 A H 0.0000
106 R H 0.0000
107 R H 0.0000
108 G H -0.2325
109 S H -0.3495
110 G H -0.3479
113 W H 0.0573
114 Y H 0.2996
115 P H 0.0000
116 D H -0.2061
117 Y H -0.0558
118 W H -0.5105
119 G H 0.0000
120 Q H -1.3310
121 G H -0.5626
122 T H 0.0000
123 L H 0.5116
124 V H 0.0000
125 T H -0.3435
126 V H 0.0000
127 S H -1.0933
128 S H -1.1927
1 N L -1.8704
2 I L -1.7793
3 Q L -1.8498
4 M L 0.0000
5 T L -0.9533
6 Q L -0.7971
7 S L -0.5623
8 P L -0.6721
9 S L -0.8383
10 S L -1.0097
11 L L -0.6036
12 S L -0.9973
13 A L 0.0000
14 S L -0.7849
15 V L 0.3149
16 G L -0.8461
17 D L -2.0263
18 R L -2.4160
19 V L -1.2044
20 T L -0.5715
21 I L 0.0000
22 T L -0.5580
23 C L 0.0000
24 Q L -2.0543
25 A L -1.9114
26 S L -1.9231
27 Q L -2.6231
28 D L -2.7983
29 I L 0.0000
36 S L -1.3409
37 N L -1.0680
38 Y L -0.2548
39 L L 0.0000
40 N L 0.0000
41 W L 0.0000
42 Y L 0.0000
43 Q L -0.8892
44 Q L 0.0000
45 K L -1.6148
46 P L -1.0600
47 G L -1.6158
48 K L -2.6295
49 A L -1.7417
50 P L 0.0000
51 K L -1.9943
52 L L 0.0000
53 L L 0.0000
54 I L 0.0000
55 Y L -0.3460
56 D L -0.9720
57 A L 0.0000
65 S L -0.9421
66 N L -1.2495
67 L L -0.4720
68 E L -0.6069
69 T L -0.4125
70 G L -0.4883
71 V L -0.4577
72 P L -0.4667
74 S L -0.5328
75 R L -0.9378
76 F L 0.0000
77 S L -0.5601
78 G L -0.5841
79 S L -0.7757
80 G L -0.7499
83 S L -1.0875
84 G L -1.6464
85 T L -1.9543
86 D L -1.6955
87 F L 0.0000
88 T L -0.4905
89 F L 0.0000
90 T L -0.5548
91 I L 0.0000
92 S L -1.3666
93 S L -1.2183
94 L L 0.0000
95 Q L -0.4344
96 P L -0.5170
97 E L -1.5924
98 D L 0.0000
99 I L 0.1691
100 A L 0.0000
101 T L -0.6336
102 Y L 0.0000
103 Y L 0.0000
104 C L 0.0000
105 Q L 0.0000
106 H L 0.0000
107 Y L -0.3689
108 D L -1.4221
109 N L -1.5043
114 L L -0.9537
115 P L -1.2010
116 L L 0.0000
117 T L -0.5731
118 F L 0.0000
119 G L 0.0000
120 G L -1.0443
121 G L -1.2583
122 T L 0.0000
123 K L -1.4189
124 V L 0.0000
125 D L -0.8705
126 I L -0.3528
127 K L -1.4702
Download PDB file
View in 3Dmol

Automated mutations analysis - charged mutations

In the automated mutations mode, the server selects aggregation prone resides and each selected residue is mutated to glutamic acid, lysine, aspartic acid and arginine. The table below shows 2 best scored mutants for each mutated residue. Protein variants are ordered according to the mutation effect they had on protein stability (energetic effect) together with the difference in the average per-residue aggregation score between the wild type and the mutant (in the table green values indicate a positive change, grey are neutral, and orange/red mean destabilizing or more aggregation prone mutants).
Summary for all the mutants can be found in this CSV file .

Mutant
Energetic effect
Score comparison
VK15L -1.7515 -0.051 View CSV PDB
VR15L -1.3712 -0.0532 View CSV PDB
VK12H -0.2328 -0.0542 View CSV PDB
VR12H -0.11 -0.0564 View CSV PDB
TD29H -0.7966 -0.0224 View CSV PDB
TE29H -0.4676 -0.0233 View CSV PDB
LR123H 0.0147 -0.0415 View CSV PDB
VK101H 0.0127 -0.0196 View CSV PDB
VR101H 0.0545 -0.0231 View CSV PDB
LK123H 0.0913 -0.0354 View CSV PDB
YR28H 0.8248 -0.0434 View CSV PDB
YD28H 0.7976 -0.0392 View CSV PDB